THEY came together in what seemed like a perfect marriage: earnest former hippies and Whole Foods, the clean, well-lighted version of the old natural food store. The chain’s stores were filled with organic foods and socially responsible ingredients. They were decorated with pastoral scenes of the local farmers who sold to them; signage explained why local and organic are better for the environment.

The food may have been more expensive, but for many shoppers it was worth it. Since opening its first store in Austin, Tex., in 1980, Whole Foods has grown from a small business to a mega-chain with 193 stores, capping its rise last week with a deal to acquire the 110 stores of its largest rival, Wild Oats.

While many shoppers find the new stores exhilarating places to shop, the company also faces critics who feel it has strayed from its original vision. In angry postings on blogs, they charge that the store is not living up to its core values — in particular, protecting the environment and supporting organic agriculture and local farmers. In interviews, some of the customers who describe themselves as committed to these values say they have become disillusioned and taken their business elsewhere.

“They are at such a level you expect the best from them, and if you don’t live up to it, people notice,” said Todd Hale, a senior vice president of consumer and shopper insights for Nielsen, the market research company. “Being first gives you a competitive advantage. But it also means somebody is going to follow you and catch up with you.”

Bill Bishop, president of Willard Bishop Consulting, a retail food consulting firm, said that Whole Foods has drifted toward the middle, which has made the store more popular with a broader range of people. Many of today’s Whole Foods shoppers are more interested in prepared foods than in whether the eggs are organic. But that carries a downside. “The folks truly devoted to organic and natural can’t get them all in Whole Foods and have to go somewhere else,” he said.

“There is a segment of shoppers,” he added, “who have moved ahead of Whole Foods. They think it is important to have a smaller carbon footprint and to want to help small farmers.” He said that John Mackey, the chief executive officer and co-founder of Whole Foods, “is lagging behind his leading shoppers.”

Wall Street has also become a bit disillusioned, and the stock has dropped by nearly 40 percent in the last year. Whole Foods faces competition from chains like Trader Joe’s, Wegmans, Safeway and Kroger, stores which have successfully copied many of its strategies: organic and natural products, expanded prepared foods and attentive service. Those stores have ample opportunity to capture the Whole Foods shopper. Mr. Hale of Nielsen said that even dedicated Whole Foods shoppers make many trips to other food stores because they tend to see Whole Foods as a “special occasion” trip.

Some former fans complain that Whole Foods is paying less attention to quality, and ignoring local produce.

Last year the author Michael Pollan called Mr. Mackey hypocritical in his book “The Omnivore’s Dilemma” for marketing organic and sustainable values while buying most of the produce from agribusiness giants like Earthbound Farm and Cal-Organic.

Officials of Whole Foods declined to comment for this article, but the company is apparently trying to respond to complaints from shoppers, articulated by Mr. Pollan. In an exchange of letters with Mr. Pollan, Mr. Mackey said that he agreed with him, at least in part.

“Whole Foods needs to do a better job of helping local growers sell directly to our stores without going through our distribution center,” he wrote, and he said he was making it a priority.

Signs have gone up in the company’s markets extolling the virtues of locally grown produce; foragers have been hired to seek out local farmers; the company has offered $10 million a year in low-interest loans to help small farmers produce more and stand-alone stores will open their parking lots to farmers’ markets on Sundays.

Mr. Mackey also drew Mr. Pollan’s attention to the company’s standards for animal compassion that have made the availability of pasture for animals a requirement and, he said, “one of the core values.”

But a recent attempt by Whole Foods to buy directly from ranchers suggests that, when it comes to doing business with individual farms, the company is still finding its way.

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Only a small amount of the organic pasture-raised beef sold by Whole Foods is American; the rest comes from abroad. In 2006, in an effort to establish sources for more locally raised meat, Mr. Mackey hired Andrew Gunther as what he called “an animal-compassionate field buyer.”

Mr. Gunther met with a group of ranchers in Omaha in October. Angela Jackson-Pridie, a grass-fed cattle expert in Vermillion, S.D., who took notes at the meeting, said he told them that individual Whole Foods stores would buy sides of beef or smaller sections directly from producers. But ranchers said that other executives in the company told them in January that Whole Foods would buy only certain parts of the animals, leaving the ranchers to market the rest themselves. Mr. Gunther did not return calls seeking comment.

Allen Williams, chief operating officer of Tallgrass Beef Company in Kansas, which has been trying to sell Whole Foods its beef, said, “the company backed way off what Gunther said. Within Whole Foods there is a monumental internal struggle to decide how they are going to do business in the protein sector.”

Whole Foods buys its private label milk from Cropp, a cooperative of organic family farmers who receive high marks from the Cornucopia Institute, a nonprofit agricultural policy research group, for humane treatment of organic cows.

A spokeswoman for Horizon said the company is in compliance with Agriculture Department standards.

When the public learned that farmed salmon has color added to its feed to make this otherwise grayish fish look like wild salmon, its much pricier cousin, Whole Foods said it would put “color added” on labels for farmed salmon. But visits to many Whole Foods stores over the last four years revealed that “color added” does not always appear on the labels of the farmed salmon, an error probably made at the store level. When employees behind the fish counters at several stores were asked if the farmed salmon had color added they were unable to answer.

In tours of eight Whole Foods stores in the Washington, D.C., area and in New York City and suburbs over the last several months, other problems suggested inattention to detail. One-third of the Yukon Gold potatoes in one display had turned green; some sweet potatoes were shriveled; cherry tomatoes in net bags were wrinkled; net bags of organic lemons contained several that were past their prime; and packaged haricots verts were brown. Six containers of one brand of yogurt available for purchase in the Bethesda, Md., store on Jan. 21 were stamped with a “use by” date of Dec. 28.

On that same day Elise Klein, who considers herself a devoted Whole Foods shopper, was returning shredded cheese, yogurt, cereal and several other items at that store, demanding a refund because all of them were out of date. “You guys need to monitor yourselves better,” she said.

In an interview later, Ms. Klein said that she was still a fan of the chain. “It’s gotten a bit more commercial,” she said. “I don’t mind that it’s more expensive but now I am going to look more carefully. But I still love it here.”

For some current and former customers, complaints about the prices and quality at Whole Foods are a staple of conversation. The store often comes up on a mothers’ blog in an area south of San Francisco, said Caryn Coleman, a stay-at-home mother of two in Mountain View, Calif.

“Produce is no longer consistently good,” Ms. Coleman said. “I can no longer count on it. Because I feel I pay more there I really expect it to be as good as a farmer’s market but sometimes it’s mushy, sometimes it’s old and sometimes it’s good. I think I use organic as proxy for a bunch of other things, like locally grown and fresher, but I’m just beginning to find out I really need to go to farmers’ markets if I want these things. I only go to Whole Foods when I can’t find a product anywhere else.”

The chain still has more fans than detractors. Lisa Shulman, a student in New York, says she can find things at the Columbus Circle Whole Foods she can’t get elsewhere.

“It’s one stop shopping,” she said. “ It’s comfortable and appealing to the eyes. I can’t say I’ve ever had anything bad here.”

A version of this article appears in print on , on Page F5 of the New York edition with the headline: Is Whole Foods Straying From Its Roots?. Order Reprints|Today's Paper|Subscribe